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Article: Structural variants and modifications of hammerhead ribozymes targeting influenza A virus conserved structural motifs.

Czapik, Tomasz / Piasecka, Julita / Kierzek, Ryszard / Kierzek, Elzbieta

2022 Volume 29, Page(s) 64–74

Abstract: The naturally occurring structure and biological functions of RNA are correlated, which includes hammerhead ribozymes. We proposed new variants of hammerhead ribozymes targeting conserved structural motifs of segment 5 of influenza A virus (IAV) (+)RNA. ... ...

Abstract	The naturally occurring structure and biological functions of RNA are correlated, which includes hammerhead ribozymes. We proposed new variants of hammerhead ribozymes targeting conserved structural motifs of segment 5 of influenza A virus (IAV) (+)RNA. The variants carry structural and chemical modifications aiming to improve the RNA cleavage activity of ribozymes. We introduced an additional hairpin motif and attempted to select ribozyme-target pairs with sequence features that enable the potential formation of the
Language	English
Publishing date	2022-05-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	2662631-7
ISSN	2162-2531
ISSN	2162-2531
DOI	10.1016/j.omtn.2022.05.035
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Article ; Online: Conscious uncoupling of riboswitch functions.

Kierzek, Elzbieta / Kierzek, Ryszard

The Journal of biological chemistry

2020 Volume 295, Issue 9, Page(s) 2568–2569

Abstract: Riboswitches alter gene expression in response to ligand binding, coupling sensing and regulatory functions to help bacteria respond to their environment. The structural determinants of ligand binding in the prequeuosine (7-aminomethyl-7-deazaguanine, ... ...

Abstract	Riboswitches alter gene expression in response to ligand binding, coupling sensing and regulatory functions to help bacteria respond to their environment. The structural determinants of ligand binding in the prequeuosine (7-aminomethyl-7-deazaguanine, preQ
MeSH term(s)	Bacteria/drug effects ; Bacteria/genetics ; Biophysical Phenomena/genetics ; Gene Expression Regulation/drug effects ; Lactobacillus rhamnosus/drug effects ; Lactobacillus rhamnosus/genetics ; Ligands ; Mutation/genetics ; Nucleic Acid Conformation/drug effects ; Pyrimidinones/pharmacology ; Pyrroles/pharmacology ; Riboswitch/drug effects ; Riboswitch/genetics
Chemical Substances	7-(aminomethyl)-7-deazaguanine ; Ligands ; Pyrimidinones ; Pyrroles ; Riboswitch
Language	English
Publishing date	2020-02-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.H120.012787
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Article ; Online: Short 2'-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA production in vitro and in vivo.

Koralewska, Natalia / Corradi, Eloina / Milewski, Marek C / Masante, Linda / Szczepanska, Agnieszka / Kierzek, Ryszard / Figlerowicz, Marek / Baudet, Marie-Laure / Kurzynska-Kokorniak, Anna

Nucleic acids research

2024

Abstract: MicroRNAs (miRNAs) that share identical or near-identical sequences constitute miRNA families and are predicted to act redundantly. Yet recent evidence suggests that members of the same miRNA family with high sequence similarity might have different ... ...

Abstract	MicroRNAs (miRNAs) that share identical or near-identical sequences constitute miRNA families and are predicted to act redundantly. Yet recent evidence suggests that members of the same miRNA family with high sequence similarity might have different roles and that this functional divergence might be rooted in their precursors' sequence. Current knock-down strategies such as antisense oligonucleotides (ASOs) or miRNA sponges cannot distinguish between identical or near identical miRNAs originating from different precursors to allow exploring unique functions of these miRNAs. We here develop a novel strategy based on short 2'-OMe/LNA-modified oligonucleotides to selectively target specific precursor molecules and ablate the production of individual members of miRNA families in vitro and in vivo. Leveraging the highly conserved Xenopus miR-181a family as proof-of-concept, we demonstrate that 2'-OMe/LNA-ASOs targeting the apical region of pre-miRNAs achieve precursor-selective inhibition of mature miRNA-5p production. Furthermore, we extend the applicability of our approach to the human miR-16 family, illustrating its universality in targeting precursors generating identical miRNAs. Overall, our strategy enables efficient manipulation of miRNA expression, offering a powerful tool to dissect the functions of identical or highly similar miRNAs derived from different precursors within miRNA families.
Language	English
Publishing date	2024-04-27
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkae284
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Article ; Online: Identification and Structural Aspects of G-Quadruplex-Forming Sequences from the Influenza A Virus Genome.

Tomaszewska, Maria / Szabat, Marta / Zielińska, Karolina / Kierzek, Ryszard

International journal of molecular sciences

2021 Volume 22, Issue 11

Abstract: Influenza A virus (IAV) causes seasonal epidemics and sporadic pandemics, therefore is an important research subject for scientists around the world. Despite the high variability of its genome, the structure of viral RNA (vRNA) possesses features that ... ...

Abstract	Influenza A virus (IAV) causes seasonal epidemics and sporadic pandemics, therefore is an important research subject for scientists around the world. Despite the high variability of its genome, the structure of viral RNA (vRNA) possesses features that remain constant between strains and are biologically important for virus replication. Therefore, conserved structural motifs of vRNA can represent a novel therapeutic target. Here, we focused on the presence of G-rich sequences within the influenza A/California/07/2009(H1N1) genome and their ability to form RNA G-quadruplex structures (G4s). We identified 12 potential quadruplex-forming sequences (PQS) and determined their conservation among the IAV strains using bioinformatics tools. Then we examined the propensity of PQS to fold into G4s by various biophysical methods. Our results revealed that six PQS oligomers could form RNA G-quadruplexes. However, three of them were confirmed to adopt G4 structures by all utilized methods. Moreover, we showed that these PQS motifs are present within segments encoding polymerase complex proteins indicating their possible role in the virus biology.
MeSH term(s)	Computational Biology ; G-Quadruplexes ; Genome, Viral/drug effects ; Genome, Viral/genetics ; Humans ; Influenza A Virus, H1N1 Subtype/genetics ; Influenza A virus/drug effects ; Influenza A virus/genetics ; Influenza, Human/genetics ; Influenza, Human/pathology ; RNA, Viral/genetics ; Virus Replication/drug effects ; Virus Replication/genetics
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-06-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22116031
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Article: A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N6-Methyladenosine

Szabat, Marta / Prochota, Martina / Kierzek, Ryszard / Kierzek, Elzbieta / Mathews, David H.

Journal of molecular biology. 2022 May 07,

2022

Abstract: RNA folding free energy change parameters are widely used to predict RNA secondary structure and to design RNA sequences. These parameters include terms for the folding free energies of helices and loops. Although the full set of parameters has only been ...

Abstract	RNA folding free energy change parameters are widely used to predict RNA secondary structure and to design RNA sequences. These parameters include terms for the folding free energies of helices and loops. Although the full set of parameters has only been traditionally available for the four common bases and backbone, it is well known that covalent modifications of nucleotides are widespread in natural RNAs. Covalent modifications are also widely used in engineered sequences. We recently derived a full set of nearest neighbor terms for RNA that includes N⁶-methyladenosine (m⁶A). In this work, we test the model using 98 optical melting experiments, matching duplexes with or without N⁶-methylation of A. Most experiments place RRACH, the consensus site of N⁶-methylation, in a variety of contexts, including helices, bulge loops, internal loops, dangling ends, and terminal mismatches. For matched sets of experiments that include either A or m⁶A in the same context, we find that the parameters for m⁶A are as accurate as those for A. Across all experiments, the root mean squared deviation between estimated and experimental free energy changes is 0.67 kcal/mol. We used the new experimental data to refine the set of nearest neighbor parameter terms for m⁶A. These parameters enable prediction of RNA secondary structures including m⁶A, which can be used to model how N⁶-methylation of A affects RNA structure.
Keywords	Gibbs free energy ; RNA ; models ; molecular biology ; nucleotides ; prediction
Language	English
Dates of publication	2022-0507
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167632
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Article ; Online: A Structural Potential of Rare Trinucleotide Repeat Tracts in RNA.

Magner, Dorota / Nowak, Rafal / Lenartowicz Onyekaa, Elzbieta / Pasternak, Anna / Kierzek, Ryszard

International journal of molecular sciences

2022 Volume 23, Issue 10

Abstract: Among types of trinucleotide repeats, there is some disproportion in the frequency of their occurrence in the human exome. This research presents new data describing the folding and thermodynamic stability of short, tandem RNA repeats of 23 types, ... ...

Abstract	Among types of trinucleotide repeats, there is some disproportion in the frequency of their occurrence in the human exome. This research presents new data describing the folding and thermodynamic stability of short, tandem RNA repeats of 23 types, focusing on the rare, yet poorly analyzed ones. UV-melting experiments included the presence of PEG or potassium and magnesium ions to determine their effect on the stability of RNA repeats structures. Rare repeats predominantly stayed single-stranded but had the potential for base pairing with other partially complementary repeat tracts. A coexistence of suitably complementary repeat types in a single RNA creates opportunities for interaction in the context of the secondary structure of RNA. We searched the human transcriptome for model RNAs in which different, particularly rare trinucleotide repeats coexist and selected the
MeSH term(s)	Base Pairing ; Humans ; RNA/chemistry ; RNA/genetics ; Thermodynamics ; Trinucleotide Repeats
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2022-05-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23105850
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Article ; Online: A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N

Szabat, Marta / Prochota, Martina / Kierzek, Ryszard / Kierzek, Elzbieta / Mathews, David H

Journal of molecular biology

2022 Volume 434, Issue 18, Page(s) 167632

Abstract	RNA folding free energy change parameters are widely used to predict RNA secondary structure and to design RNA sequences. These parameters include terms for the folding free energies of helices and loops. Although the full set of parameters has only been traditionally available for the four common bases and backbone, it is well known that covalent modifications of nucleotides are widespread in natural RNAs. Covalent modifications are also widely used in engineered sequences. We recently derived a full set of nearest neighbor terms for RNA that includes N
MeSH term(s)	Adenosine/analogs & derivatives ; Adenosine/chemistry ; Entropy ; RNA/chemistry ; RNA Folding
Chemical Substances	RNA (63231-63-0) ; N-methyladenosine (CLE6G00625) ; Adenosine (K72T3FS567)
Language	English
Publishing date	2022-05-16
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167632
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Article ; Online: Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3'-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides.

Kauffmann, Andrew D / Kennedy, Scott D / Moss, Walter N / Kierzek, Elzbieta / Kierzek, Ryszard / Turner, Douglas H

RNA (New York, N.Y.)

2022 Volume 28, Issue 4, Page(s) 508–522

Abstract: Influenza A kills hundreds of thousands of people globally every year and has the potential to generate more severe pandemics. Influenza A's RNA genome and transcriptome provide many potential therapeutic targets. Here, nuclear magnetic resonance (NMR) ... ...

Abstract	Influenza A kills hundreds of thousands of people globally every year and has the potential to generate more severe pandemics. Influenza A's RNA genome and transcriptome provide many potential therapeutic targets. Here, nuclear magnetic resonance (NMR) experiments suggest that one such target could be a hairpin loop of 8 nucleotides in a pseudoknot that sequesters a 3' splice site in canonical pairs until a conformational change releases it into a dynamic 2 × 2-nt internal loop. NMR experiments reveal that the hairpin loop is dynamic and able to bind oligonucleotides as short as pentamers. A 3D NMR structure of the complex contains 4 and likely 5 bp between pentamer and loop. Moreover, a hairpin sequence was discovered that mimics the equilibrium of the influenza hairpin between its structure in the pseudoknot and upon release of the splice site. Oligonucleotide binding shifts the equilibrium completely to the hairpin secondary structure required for pseudoknot folding. The results suggest this hairpin can be used to screen for compounds that stabilize the pseudoknot and potentially reduce splicing.
MeSH term(s)	Base Sequence ; Humans ; Influenza, Human/genetics ; Magnetic Resonance Spectroscopy ; Nucleic Acid Conformation ; Oligonucleotides ; RNA Splice Sites/genetics ; RNA, Messenger/metabolism
Chemical Substances	Oligonucleotides ; RNA Splice Sites ; RNA, Messenger
Language	English
Publishing date	2022-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.078951.121
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Article ; Online: In vivo secondary structural analysis of Influenza A virus genomic RNA.

Mirska, Barbara / Woźniak, Tomasz / Lorent, Dagny / Ruszkowska, Agnieszka / Peterson, Jake M / Moss, Walter N / Mathews, David H / Kierzek, Ryszard / Kierzek, Elzbieta

Cellular and molecular life sciences : CMLS

2023 Volume 80, Issue 5, Page(s) 136

Abstract: Influenza A virus (IAV) is a respiratory virus that causes epidemics and pandemics. Knowledge of IAV RNA secondary structure in vivo is crucial for a better understanding of virus biology. Moreover, it is a fundament for the development of new RNA- ... ...

Abstract	Influenza A virus (IAV) is a respiratory virus that causes epidemics and pandemics. Knowledge of IAV RNA secondary structure in vivo is crucial for a better understanding of virus biology. Moreover, it is a fundament for the development of new RNA-targeting antivirals. Chemical RNA mapping using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) coupled with Mutational Profiling (MaP) allows for the thorough examination of secondary structures in low-abundance RNAs in their biological context. So far, the method has been used for analyzing the RNA secondary structures of several viruses including SARS-CoV-2 in virio and in cellulo. Here, we used SHAPE-MaP and dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) for genome-wide secondary structure analysis of viral RNA (vRNA) of the pandemic influenza A/California/04/2009 (H1N1) strain in both in virio and in cellulo environments. Experimental data allowed the prediction of the secondary structures of all eight vRNA segments in virio and, for the first time, the structures of vRNA5, 7, and 8 in cellulo. We conducted a comprehensive structural analysis of the proposed vRNA structures to reveal the motifs predicted with the highest accuracy. We also performed a base-pairs conservation analysis of the predicted vRNA structures and revealed many highly conserved vRNA motifs among the IAVs. The structural motifs presented herein are potential candidates for new IAV antiviral strategies.
MeSH term(s)	Humans ; Influenza A Virus, H1N1 Subtype/genetics ; COVID-19 ; SARS-CoV-2/genetics ; Influenza A virus/genetics ; RNA, Viral/genetics ; Genomics
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-05-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-023-04764-1
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Article ; Online: Parallel-stranded DNA and RNA duplexes - structural features and potential applications.

Szabat, Marta / Kierzek, Ryszard

The FEBS journal

2017

Abstract: Nowadays, decades after the discovery of the right-handed B form of DNA, it is well known that nucleic acids have great conformational flexibility, exhibiting a large degree of variation in their structure. In nature, DNA and RNA exist in an antiparallel ...

Abstract	Nowadays, decades after the discovery of the right-handed B form of DNA, it is well known that nucleic acids have great conformational flexibility, exhibiting a large degree of variation in their structure. In nature, DNA and RNA exist in an antiparallel orientation, stabilized by Watson-Crick base pairs. However, in some cases, nucleic acid fragments with specific nucleotide sequences can adopt a parallel orientation involving non-canonical base pairing. Interestingly, parallel-stranded duplexes have been found in specific chromosome regions. Furthermore, parallel oriented regions have also been found in bacterial (Escherichia coli, Listeria innocua) and insect genomes (Drosophila melanogaster). These unusual structures could have a remarkable evolutionary role, as well as significant impact on biological processes. For example, parallel stretches were shown to be involved in processing the 3' ends of mRNAs and in specific gene silencing. Moreover, certain types of parallel-stranded duplexes may be useful tools, with several practical applications. They can constitute excellent templates for the formation of other structures and for the development of antigene and antisense approaches.
Language	English
Publishing date	2017-08-03
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.14187
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